"Fundamentals have kept the funds positioned short corn and wheat for most of 2016 with global stocks record large while the funds have shifted to long soybean stance based on strong global demand for vegetable oils," said Kim Rugel, at Benson Quinn Commodities.
Chicago wheat futures ended the year down some 13%, under pressure from the huge global harvest.
March wheat future settled up 1.0% on the day, at $4.08 a bushel.
And corn futures finished the year down about 2%, down for the fourth straight year in a row.
March corn futures settled up 0.4% on the day, at $3.52 a bushel.
But soybeans finished the year up some 14%, as January soybean futures finished the day down 0.6%, at $9.97 a bushel.
Brazilian drought
It was a day for end of year positioning, but attention was also focused on South America.
"Coming back from New Year holiday, focus will shift to South American weather where dryness in northeastern Brazil is raising some concern," said Ms Rugel.
"Early New Year trade will focus on South American weather," agreed Richard Feltes at RJ O'Brien.
At Country Futures, Darrell Holaday noted "a lot of debate around the Brazilian weather outlook".
"The models for 11-15 days out have turned wetter in the last two days for some key dry areas in the eastern and northeastern production areas," Mr Holaday said.
"Those that are bullish contend it will not be enough rain. Keep in mind that this areas normal rainfall in per month is around eight inches. So 50% below normal is still four inches."
2This is what most of the debate centres around as the market sees four inches as plenty of moisture for soybeans in a month," said Mr Holaday.
"Others argue it will trim yields."
US frost
Mr Feltes also noted the "looming" prospect of the January supply and demand figures from the US Department of Agriculture, "where trade is bracing for negative news on first quarter corn feed use while soy market knows a lower than expected winter wheat area implies even more bean acres in 2017".
And weather concerns are emerging in the US Plains.
"Cold temperatures appear back in the forecast in the 6-10 model for the Plains, and with little snowpack is some areas, talks winter wheat kill are likely next week as the temperatures move through," said Paul Georgy at Allendale.
Weak soybean export sales
US wheat export sales, delayed due to the long weekend, came in above expectations, at 568,000 tonnes.
Corn export sales came in in line with expectations, at 958,600 tonnes.
US soybean export sales missed expectations slightly, at 974,100 tonnes.
"Sales were only half of what they were last week and this was the lowest sales total in 7 weeks," said Joe Lardy, at CHS Hedging.
"The bean and corn numbers are down from prior weeks but one can attribute that to Christmas holiday," said Ms Rugel.
Lack of global demand gives cocoa a rotten year
Cocoa futures were the big loser of 2016, finishing the year down some 33%.
Prices have taken a pacing thanks to the prospect of a big West African crop, and a moribund global demand, which are pushing the market into surplus.
March New York cocoa settled down 1.8%, at $2,126 a tonne.
March London cocoa futures settled down 2.0%, at 1,732 pounds a tonne.
Dry Asia
Sugar futures, in comparison, were a big winner, as traders caught on to the current global production deficit, caused in part by the lingering effects of the Asian drought caused by last winter's El Nino, with front-month New York futures finishing up some 28%.
March raw sugar settled up 0.1%, at 19.51 cents a pound.
March whites sugar futures settled up 0.6%, at $524.20 a tonne.
Tighter robusta supplies
But sugar gains couldn't match the huge rise in robusta in 2016.
Robusta futures have rocketed thanks to plummeting Brazilian production, and continued concerns over the crop in Vietnam.
March robusta coffee futures settled up 1.0% on the day $2,138 a tonne, leaving prices up some 40% on the year.
Arabica coffee futures finished the year up 8%, thanks to support from the robusta markets.
March arabica coffee settled up 1.2%, at 137.05 cents a pound.